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Sample GSM857412 Query DataSets for GSM857412
Status Public on Mar 26, 2012
Title MM_ND2_rep1_batch2
Sample type RNA
Source name MEF transduced with NeuroD2 lentivirus
Organism Mus musculus
Characteristics cell type: Neuronally differentiated MEF cells
Treatment protocol P19 cells and MEFs were infected with lentivirus in media containing polybrene (final concentration 8 µg /ml), and after 24 hours the cells were switched into fresh media. MEFs transduced with MyoD were switched to differentiation media (1% heat inactivated horse serum, 10 μg/mL insulin, 10 μg/mL transferrin) 48 hours after infection.
Growth protocol P19 cells were maintained in MEMα as previously described (Farah et al., 2000, PUBMED ID 10648228), and MEFs derived from Myod-/-/Myf5-/- mice were maintained in DMEM with 10% FBS.
Extracted molecule total RNA
Extraction protocol Neuronally differentiated P19 cells were harvested 72 hours after infection. MEFs were harvested 36-40 hours after switching to differentiation media.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Affymetrix One-Cycle Eukaryotic Target Labeling Assay.
Hybridization protocol Standard Affymetrix hybridization protocol
Scan protocol Standard Affymetrix scanning protocol
Description 2.MM.ND.1
Data processing Probe intensities were corrected, normalized, and summarized by the simpleaffy package of Bioconductor (Wilson and Miller,2005). Differentially expressed genes were identified by the LIMMA package of Bioconductor (Wettenhall and Smyth, 2004).
Submission date Jan 06, 2012
Last update date Apr 05, 2017
Contact name Stephen Tapscott
Organization name Fred Hutch Cancer Research Center
Department Human Biology
Lab Tapscott
Street address 1100 Fairview N. Ave
City Seattle
State/province WASHINGTON
ZIP/Postal code 98103
Country USA
Platform ID GPL1261
Series (2)
GSE34907 Genetic and epigenetic determinants of neurogenesis and myogenesis [expression profiling]
GSE34908 Genetic and epigenetic determinants of neurogenesis and myogenesis

Data table header descriptions
VALUE RMA normalized

Data table
1415670_at 10.85466918
1415671_at 11.89485578
1415672_at 11.81289768
1415673_at 9.742754387
1415674_a_at 10.24682691
1415675_at 9.860948986
1415676_a_at 11.52300044
1415677_at 9.769325357
1415678_at 11.42804054
1415679_at 11.52639158
1415680_at 9.703908684
1415681_at 10.11911543
1415682_at 8.6415758
1415683_at 11.32960709
1415684_at 9.192260047
1415685_at 9.48315751
1415686_at 9.554589265
1415687_a_at 13.61718048
1415688_at 10.91978793
1415689_s_at 9.507561987

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.

Supplementary file Size Download File type/resource
GSM857412_MG430_2.0_04_MM_N-1.CEL.gz 6.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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